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BCMB20002 Biochemistry > Protein Structure > Flashcards

Protein Structure Flashcards

1
Q

What makes up proteins?

A

Amino Acid Residues

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2
Q

Why can it be difficult to annotate a gene?

A

o One gene several proteins
o Two genes overlapping
o One protein multiple functions

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3
Q

How can proteins be post-translationallymodified?

A
  • Phosphorylation (signalling)
  • Glycosylation (protection, signalling)
  • Proteolytic Cleavage (trafficking sequences)
  • Acylation (fatty acids, localisation, regulation)
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4
Q

Are proteins static? What is the best way to describe proteins in terms of motion?

A

No.

• Soft matter with flexibility

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5
Q

What are the key things to remember about the property of proteins?

A
  • One gene does not always equal one protein
  • All cells have same DNA but not always same protein content
  • Proteins are soft matter and both flexible with the potential to be highly structured
  • Can be post-translationallly modified and their function can be changed
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6
Q

What are the levels of protein structure?

A 
Primary
•	Amino acid sequence from N-terminus to C-terminus
Secondary
•	Local areas of regular ordered structure 
Tertiary
•	3D fold of subunit
Quaternary
•	Organisation of subunits
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7
Q

Which way should an AA sequence be read in terms of terminals?

A

From N to C

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8
Q

What is the general structure of an amino acid?

A 
•	L configuration, not D 
•	α Carbon in middle with α hydrogen coming towards, carboxylate group (COO-), R group (R), Amine group (NH3+)- CORN
•	Zwitterionic: 
deprotonate 
•	Amino Acid residue: -HN-CHR-CO-
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9
Q

What is zwitterionic?

A

o neutral with no net charge at neutral pH. Both carboxylate and amine can be ionised
o Add protons (more acid), lower pka/pH, protonate
o Remove protons (more base), rise pKa/pH,

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10
Q

What is L configuration?

A

can be synthesised from L-glyceraldehyde

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11
Q

How can groups be protonated or de-protonated?

A

Add acid (protonate, make more negative, lower pH and pKa, NH3+ and COOH)

Add base (deprotonate, make more postive, raise pH and pKa, NH2 and COO-)

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12
Q

Can NH2-(CHR)-COOH exist? Why?

A

No. It’s not zwitterionic. No charges to balance.

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13
Q

How do pH and pKa interact?

A
  • pH = pKa + log [A-] / [HA]
  • When [A-] = [HA], pH = pKa (log1 = 0)
  • pH = pKa : [COOH] = [COO-]
  • pH > pKa : [COOH] < [COO-] more acid
  • pH < pKa : [COOH] > [COO-]
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14
Q

Where on a protein will hydrophobic or hydrophilic residues be found?

A
  • Hydrophobic : inside protein

* Hydrophilic: outside protein

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15
Q

Which amino acids are hydrophilic (charged, polar)?

A 
•	Acidic (-charge at neutral pH, low pKa, carboxylate)
o	Aspartate (Asp, D)
o	Glutamate (Glu, E)
•	Basic (+charge at neutral pH, higher pKa) 
o	Lysine (Lys, K)
o	Arginine (Arg, R)
o	Histidine (His, H)

Hydrophillic = charged and polar

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16
Q

Which amino acids are hydrophilic (neutral, polar)?

A 
•	Carboxamide 
o	Asparagine (Asn, N) 
o	Glutamine (Gln, Q) 
•	Hydroxyl
o	Serine (Ser, S)
o	Threonine (Thr, T)
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17
Q

Which amino acids are hydrophobic (aliphatic)?

A
  • All methyl groups
  • Alanine (Ala, A)
  • Valine (Val, V)
  • Leucine (Leu, L)
  • Isoleucine (Ile, I)
  • Methionine (Met, M)
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18
Q

Which amino acids are hydrophobic (aromatic) ?

A 
•	Phenyl
o	Phenylalanine (Phe, F)
•	Phenol
o	Tyrosine (Tyr, Y) 
•	Indole
o	Tryptophan (Trp, W)
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19
Q

Which amino acids fit the ‘other’ category?

A 
•	No R group
o	Glycine (Gly, G)
•	Thiol
o	Cysteine (Cys, C) 
•	Pyrrolidine
o	Proline (Pro, P)
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20
Q

Which AA residues are sometimes phosphorylated?

A

Serine, Threonine, Tyrosine

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21
Q

Which AA residues are sometimes glycosylated?

A

Asparagine, Serine, Threonine

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22
Q

What is involved in phosphorylation?

A
  • Enzymatic addition of group
  • Add phosphate
  • Regulation/amplification of biological processes
  • Changes chemical nature (polar neutral to polar negatively charged)
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23
Q

What is involved in glycosylation?

A
  • Enzymatic addition of group

* Add carbohydrate

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24
Q

What are the features of aromatic groups?

A

flat, share double bonds, sp2

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25
Q

What group is common to hydrophobic (aliphatic) amino acids?

A

Methyl group

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26
Q

What are the branched chain amino acids?

A

Valine, Leucine, Isoleucine

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27
Q

What is the largest and rarest amino acid?

A

Tryptophan

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28
Q

Which AA lacks an R group?

A

Glycine

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29
Q

Which AAs absorb UV light well?

A

Tryptophan, Tyrosine

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30
Q

Which AAs are most common?

A

Alanine, glycine, leucine

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31
Q

What is the mean MW for AA residue?

A

110

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32
Q

What are the features of the peptide bond?

A

Stable but can be hydrolysed by proteases

Partial Double Bond Character

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33
Q

What reaction forms a peptide bond? What molecule is lost during it?

A
  • Condensation reaction between COO- and NH3+

* Lose water

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34
Q

What forms the covalent structure of a protein?

A

Primary AA sequence

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35
Q

What are the features of the double bond character?

A
  • Resonance structures (C=O, C=N)
  • 1.32 A length
  • Gives rigidity and planarity
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36
Q

Which configuration (cis/trans) is favoured with peptide bonds and why?

A

Trans orientation (180)
• Four atoms of relevance: Cα(i), Cα(i-1), N(i), C (i-1)
• More stable peptides are trans (avoid steric clash)
• Α C’s on opposite sides of bonds

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37
Q

What is the general rule to calculate molecular weight of a protein?

A

number of residues X 110 = Molecular Weight

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38
Q

What is isoelectric point?

A

• pH where protein carries NO charge

39
Q

What is the net charge of a protein when pH < pI?

A

Postive

40
Q

What is the net charge of a protein when pH > pI?

A

Negative

41
Q

How does the length of a peptide influence pKa and ionisation?

A

• Longer peptide = more COOH and less NH3+
o Favourable reaction between NH3+ and COO- reduced due to distance
o COO- more remote and not free to stabilise NH3+
o Therefore the distance between pka1 (COOH) and pk2 (NH3+) decreases

42
Q

What determines if a pI is acidic or basic?

A
  • Large pI = basic

* Small pI = acidic

43
Q

How can we work out the sequence/covalent structure of a protein?

A
  • Edman degradation (remove AA and identify)
  • Mass spectrometry
  • DNA sequence but won’t show post translational modification information
44
Q

What is a torsion angle?

A

Dihedral angle
• Made up of four atoms, three bonds
• Counter clockwise = +ve
• Each peptide bond plane can be orientated to succeeding/preceding peptide bond planes by the two torsion angles φ and ψ

45
Q

What is ω?

A
  • Torsion angle of peptide bond
  • Relevant atoms: αC (i-1), C’(i-1), N(i), αC(i)
  • Cis: ω= 0
  • Trans: ω= 180
46
Q

What is φ?

A
  • Rotation around N- αC bond
  • No rotation around rigid peptide bond
  • Relevant atoms: C’(i-1), N(i), αC (i), C’ (i)
47
Q

What is ψ?

A
  • Rotation around αC-C’ bond
  • No rotation around rigid peptide bond
  • Relevant atoms: N(i), αC (i), C’ (i), N (i+1)
48
Q

Which angles characterise each residue in a protein?

A

Each residue ion protein can be characterised by a φ and ψ pair

49
Q

How can φ and ψ interact? What do steric clashes prevent?

A

• Not completely free to rotate (steric clashes restricting)

50
Q

What would φ and ψ angles of 180° result in?

A

No steric clash

51
Q

What would φ and ψ angles of 0° result in?

A

Steric Clash

52
Q

What kind of angle is favoured for φ? Why?

A

Favour φ to be negative

• Side chain opposite (no clash between side chain and carbonyl oxygen)

53
Q

What does the Ramachandran Plot show? What are the most favoured regions?

A
  • Certain angles of φ and ψ favoured
  • Favoured regions: α and β
  • α (α helices)
  • β (β sheets)
  • Forbidden regions: steric hindrance
  • Expect majority of structures in favoured regions
54
Q

How can glycine be on the right of the Ramachandran Plot?

A

No R group, no steric hindrance if + φ

55
Q

How does regular and irregular secondary structure differ?

A

Regular Secondary Structure
• Repeating φ and ψ angles for sequential residues
• Elements with repeating φ and ψ in α region =α helices
• Elements with repeating φ and ψ in β region =β strands (make up β sheets)
Irregular Secondary Structure
• Non-repeating φ and ψ angles for sequential residues
• E.g. β turn (different angles between sequential residues)

56
Q

What does 3.613 mean?

A

• 3.6 residues per turn (one every 100°), 13 atoms in H bond ring = 3.613

57
Q

What are the features of α helices?

A
  • Side chains pointed away from helix
  • Right handed
  • φ -60° and ψ-50°
  • NH and C=O in helix form internal favourable hydrogen bonds
  • Carbonyls oppositely aligned to NH
  • Amphipathic
58
Q

In αhelices, what kind of bonds are formed?

A

• NH and C=O in helix form internal favourable hydrogen bonds

59
Q

What does it mean for an α helix to be amphipathic?

A

o One side hydrophobic, one side hydrophilic

o Helical wheel

60
Q

What are the features of a β sheet?

A
  • Made from β strands
  • Strands = parallel or antiparralel to neighbours
  • φ -130° and ψ +130°
  • H bonds between C=O and NH of opposing strands
  • Outer NH and C=O not H bonded
61
Q

What are β turns? What kind of structure are they?

A
  • Irregular stricture
  • Reverse main chain
  • Mostly on surface
  • Four residues (different φ and ψ angles for i+1, i+2)
  • Stabilised by H bond between Carbonyl of i and NH of i+3
  • i+1 often proline
  • i+2 often glycine in type II
62
Q

How are type I and type II β turns different?

A

Type II
• i+2 R group on same side as i+1 (+φ)
• Expect clash
• Therefore i+2 Glycine because no R group, just H

63
Q

What was the Anfinsen experiment?

A
  • Showed AA sequence determines 3D structure
  • Unfold protein in urea and reducer (ribonuclease A)
  • Remove urea and reluctant, notice spontaneous refolding and correct disulphides reforming (expect 105 due to 8 cysteine’s, but only see 1)
  • Remove reluctant and keep urea, random disulphides form
  • Protein folds so in can position cys residues correctly
  • Weak non covalent interactions that manoeuvre protein so disulphides can form
64
Q

What is the basis of Van der Waals interactions and what is Rm?

A
  • Inside of protein = compact
  • Two atoms approach each other until reach VDW radii distance (favourable attraction up until the distance)
  • Contact distance = energy minimum = Rm
  • VDW radius varies for atoms (e.g. carbon is 1.7 Å, VDW distance between two carbon is about 4Å)
65
Q

What are hydrogen bonds?

A
  • Two electronegative atoms compete for same hydrogen
  • Donor (D) δ+
  • Acceptor (A) δ-
  • Electrostatic interaction
  • Transfer of electrons from A to H has covalent component
66
Q

What helps proteins be compact?

A

Hydrogen bonds (shorter than VDW)

67
Q

What length of hydrogen bond would be strong and mostly covalent?

A

2.2-2.5 Å

68
Q

What length of hydrogen bond would be moderate and mostly electrostatic?

A

2.5-3.2 Å

69
Q

What length of hydrogen bond would be weak and electrostatic?

A

3.2-4.0 Å

70
Q

Where can hydrogen bonds occur?

A
  • Backbone-backbone
  • Backbone-side chain
  • Side chain-side chain
  • Polar groups buried in protein must form hydrogen bonds
71
Q

What are salt bridges? What type of interaction are they?

A
  • Electrostatic interactions
  • Ionic interactions between oppositely charged groups
  • Stabilises ionic interaction
  • Charges distributed
  • pKa for residues different to typical value (bases more, acids less)
72
Q

What are hydrophobic interactions?

A

• In aqueous environment, hydrogen bond and VDW interactions between polar groups no favoured (competition with water)
• Proteins fold
o Water poor solvent for nonpolar groups (unlike organic solvents)
o Nonpolar groups cant form hydrogen bond networks
o Nonpolar groups prefer interact with other nonpolar groups

73
Q

What drives hydrophobic interactions?

A

Entropy, solvent entropy = driver

• Favourable/negative ∆G given if negative ∆H and positive ∆S (↑disorder)

74
Q

How does entropy differ between unfolded and folded proteins?

A 
Low Entropy +∆G
•	Unfolded 
•	Lots of ORDERED water molecules
•	Exposed nonpolar side chains
High Entropy -∆G
•	Folded
•	Bury non polar side chains
•	Release ordered water molecules
•	Disorder increases
75
Q

How does ∆G relate to protein folding?

A

∆G = ∆H - T∆S
• Unfolded ↔ Folded (preferred)
• ∆G = ∆H - T∆S
• ∆H: VDW and H bonds (-15 - -20kj/mol)
• ∆S: disorder of protein and solvent entropy
• ∆G: G(folded) – G(unfolded)
• Native state proteins = marginally stable

76
Q

Which methods are used to determine protein structure?

A
  • X-ray crystallography (3D crystals)
  • NMR spectroscopy (solution, solids)
  • Electron Microscopy (2D crystals)
77
Q

What are the ways to view and represent protein structure?

A 
•	Wire – line, stick 
o	Full details on position of atoms
•	Cartoon – Ribbon
o	Helix (coil) and strand (arrow) orientation and position 
•	Sphere 
o	Surface nature
o	Residue exposure
78
Q

What are the features of Myoglobin as a globular protein?

A
  • Small, oxygen binding
  • Eight α helices (different lengths, loops connect them or some β turns)
  • Well defined ordered structure
  • Most hydrophobic residues inside
79
Q

What kind of bonding can be found in Myoglobin and where?

A
  • Close contacts (VDW) between hydrophobic residues of helices
  • No main chain hydrogen bonds between helices (H bonds within helices or with side chains)
80
Q

What is the significance of the edge of Heme being exposed in myoglobin?

A

• Edge of heme exposed in order for oxidation to occur

81
Q

What are the super-secondary structures?

A
  • Repeating elements
  • α-α corner/hairpin
  • β-β hairpin
  • βαβ element
82
Q

What are the four rules of protein structure?

A
  1. Hydrophobic interactions for stability. Need at least 2 layers of secondary structure fo H20 to be excluded and hydrophobic side chains to be buried.
  2. α helices and β sheets in separate layers because backbone H bonding disallows helices to H bond to sheets.
  3. Protein segments adjacent in sequence usually adjacent in structure.
  4. β strands favour right hand twist and between two parallel strands. Connections shorter than left hand.
83
Q

What kind of connections between β strands are shorter (left or right hand)?

A

Right Hand

84
Q

What is the significance of proteins in the sequence usually being adjacent in structure?

A
  • Some exceptions
  • Non-random distribution of elements
  • Distant regions still brought together
85
Q

Why is the right handed β strand connection preferred?

A
  • Need less protein to form connection

* Conserve protein is favourable

86
Q

What is a domain? What type of core does it have?

A
  • Domain is region in tertiary structure of which evidence provides an existence independent of the rest of the protein
  • Hydrophobic core in each domain separates them from each other
  • Arrangement and order of secondary structural elements that contain single hydrophobic core
87
Q

What are the features of domains?

A
  • Size varies
  • Individual domains: individual functions possible (catalytic, binding)
  • Modular proteins, repeating domains, slightly different sequence, same fold
  • Most proteins multiple domains (teamwork)
  • Same protein domain can be found in functionally distinct proteins
  • Same shape, sequence can vary
  • So far identified 1500 unique domains
88
Q

Why is it more accurate to describe a domain as an evolutionary unit rather than structural unit?

A
  • The way new proteins arise suggests common protein ancestor
  • Individual domains further subjected to mutation, insertions, deletions, randomly
  • NO new domains created
89
Q

How can protein domains be aligned?

A
  • Based on residue identity or similarity
  • Identity: exactly same residue
  • Similarity: change to residue observed frequently or with similar phys-chem properties (ser to thr)
  • Improve alignments with gaps
90
Q

What are the reasons for gaps in protein domain alignment?

A

o Account for insertion, deletion of residues

91
Q

What are homologues?

A

o Share common protein domain ancestor, share same fold

>25% similarity = homologous

92
Q

What are orthologues and paralogues?

A

Orthologues
o Homologous proteins, same function, different species
Paralogues
o Homologus proteins, different but related functions, one organism

93
Q

How does protein structure compare for proteins that are related but have different sequences?

A
  • Sequence change = small structure change
  • Structure change much SLOWER than sequence change (sequences with >25% identity very similar structure)
  • Similar secondary and tertiary structure
  • Gaps = loop insertion within general structural fold
  • Different parts of protein mutate at different rates (conservation of functional residues)
94
Q

How can new proteins with new functions be generated?

A
  • Mix domains and mutate existing domains
  • Intragenic mutation (point, indel)
  • Gene duplication
  • DNA segment shuffle (broken, recombined)
  • Gene lateral transfer

BCMB20002 Biochemistry (7 decks)

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